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Updated: Feb 28, 2026
Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach
Published on: December 1, 2011
Results of the first international HIV-1 coreceptor proficiency panel test
Eva Heger1, Rolf Kaiser1, Elena Knops1
1Institute of Virology, University of Cologne, 50935 Cologne, Germany.
Background:
Quality Assurance (QA) programs are essential to evaluate performance in diagnostics laboratories.
Objectives:
We present the results from the first QA for HIV-1 genotypic tropism testing, organized and coordinated by the Institute of Virology at the University of Cologne.
Study Design:
12 cell culture-derived viral strains of different HIV-1 clades from the NIH AIDS Reagent Program were sent to the participants to be processed with their standard diagnostic methods Fasta files containing the V3 region sequence were centrally analyzed at the Institute of Virology, Cologne. All samples were sent in parallel for phenotypic testing.
Results:
36 laboratories from 16 countries reported genotypic results. The sequence-generation efficacy was 95.1%, while the phenotypic assays ESTA® and PhenXR only achieved results for 58.3% of the samples. All four X4 samples were identified by 31/36 laboratories, two laboratories amplified 3/4×4 samples, and three detected 2/4×4 samples. There was high concordance among the genotypic and phenotypic results, although differences in FPR values were detected. Most deficiencies in sequence editing did not result in wrong classification of X4 viruses as R5, with the exception of sample NRZ05 by laboratory 38, but in an overestimation of CXCR4 use.
Conclusions:
This demonstrates that genotypic tropism prediction is a safe procedure for clinical purposes. As we used homogeneous cell culture samples and all sequence fasta files were centrally analyzed, variations in FPR values can only be attributed to sample preparation, RT-PCR or sequence editing protocols.
